AutoCloner

Multiple sequence alignment - TraesCS3A01G032500

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Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS3A01G032500	chr3A	100.000	3087	0	0	1	3087	18817917	18821003	0.000000e+00	5701.0
1	TraesCS3A01G032500	chr3A	100.000	2089	0	0	1	2089	19267063	19264975	0.000000e+00	3858.0
2	TraesCS3A01G032500	chr3A	87.981	624	60	8	2479	3087	745905249	745905872	0.000000e+00	723.0
3	TraesCS3A01G032500	chr3A	95.844	409	11	2	1692	2095	19269652	19269245	0.000000e+00	656.0
4	TraesCS3A01G032500	chr3A	93.182	44	3	0	2090	2133	369397018	369397061	7.150000e-07	65.8
5	TraesCS3A01G032500	chr3D	94.588	1164	60	2	924	2087	17698205	17699365	0.000000e+00	1797.0
6	TraesCS3A01G032500	chr3D	85.175	1113	142	13	1000	2093	17343131	17342023	0.000000e+00	1120.0
7	TraesCS3A01G032500	chr3D	88.784	633	42	12	2477	3085	587475261	587475888	0.000000e+00	749.0
8	TraesCS3A01G032500	chr3D	91.844	282	16	5	563	843	17698087	17697812	1.340000e-103	387.0
9	TraesCS3A01G032500	chr6D	84.349	1099	158	10	1005	2093	417752071	417750977	0.000000e+00	1064.0
10	TraesCS3A01G032500	chr6D	82.684	1103	152	25	1003	2087	417775857	417776938	0.000000e+00	942.0
11	TraesCS3A01G032500	chr6D	88.718	195	21	1	2479	2672	426931385	426931191	1.430000e-58	237.0
12	TraesCS3A01G032500	chr6B	83.244	1116	163	13	992	2087	626643906	626645017	0.000000e+00	1003.0
13	TraesCS3A01G032500	chr6B	88.517	627	46	14	2476	3085	2806721	2806104	0.000000e+00	736.0
14	TraesCS3A01G032500	chr6B	88.320	625	50	11	2478	3085	309686036	309686654	0.000000e+00	728.0
15	TraesCS3A01G032500	chr6B	84.026	770	109	9	1334	2093	626489330	626488565	0.000000e+00	728.0
16	TraesCS3A01G032500	chr6A	83.258	1099	170	11	1005	2093	560192872	560191778	0.000000e+00	998.0
17	TraesCS3A01G032500	chr6A	81.125	1102	159	22	1003	2087	560444263	560445332	0.000000e+00	837.0
18	TraesCS3A01G032500	chr6A	87.967	615	51	10	2490	3087	473572138	473571530	0.000000e+00	704.0
19	TraesCS3A01G032500	chr6A	91.414	198	15	2	2476	2672	593456818	593456622	1.410000e-68	270.0
20	TraesCS3A01G032500	chr6A	84.848	231	33	2	1003	1232	560489042	560489271	6.660000e-57	231.0
21	TraesCS3A01G032500	chr1D	89.524	630	48	7	2476	3087	101104528	101105157	0.000000e+00	782.0
22	TraesCS3A01G032500	chr1D	86.240	625	54	16	2478	3085	476403354	476402745	0.000000e+00	649.0
23	TraesCS3A01G032500	chr1D	92.683	41	3	0	2093	2133	339110983	339110943	3.320000e-05	60.2
24	TraesCS3A01G032500	chr2A	89.677	620	47	7	2483	3087	25097431	25096814	0.000000e+00	774.0
25	TraesCS3A01G032500	chr2A	86.076	474	38	14	2483	2931	749798365	749797895	4.630000e-133	484.0
26	TraesCS3A01G032500	chr1A	88.052	611	55	11	2493	3087	440148309	440147701	0.000000e+00	708.0
27	TraesCS3A01G032500	chr1A	86.230	610	64	7	2476	3085	549125016	549124427	0.000000e+00	643.0
28	TraesCS3A01G032500	chr1B	87.640	623	57	10	2476	3079	16777388	16778009	0.000000e+00	706.0
29	TraesCS3A01G032500	chr3B	86.872	617	52	18	2485	3085	825637423	825636820	0.000000e+00	664.0
30	TraesCS3A01G032500	chrUn	85.191	628	48	13	2494	3085	319124385	319123767	1.220000e-168	603.0
31	TraesCS3A01G032500	chrUn	86.243	567	42	12	2494	3033	375367803	375367246	1.600000e-162	582.0
32	TraesCS3A01G032500	chrUn	83.830	235	19	9	2151	2384	38150196	38150412	4.040000e-49	206.0
33	TraesCS3A01G032500	chr4A	83.943	629	66	16	2476	3076	646515391	646516012	1.240000e-158	569.0
34	TraesCS3A01G032500	chr2D	84.326	319	23	7	2476	2770	586913376	586913691	1.400000e-73	287.0
35	TraesCS3A01G032500	chr5D	95.349	43	2	0	2091	2133	526842864	526842906	5.520000e-08	69.4
36	TraesCS3A01G032500	chr5B	97.500	40	1	0	2096	2135	486482443	486482482	5.520000e-08	69.4
37	TraesCS3A01G032500	chr5B	93.023	43	3	0	2091	2133	662602725	662602767	2.570000e-06	63.9
38	TraesCS3A01G032500	chr7B	93.023	43	3	0	2091	2133	405065534	405065576	2.570000e-06	63.9
39	TraesCS3A01G032500	chr7A	93.023	43	3	0	2093	2135	464911524	464911482	2.570000e-06	63.9
40	TraesCS3A01G032500	chr7D	91.111	45	4	0	2090	2134	607100181	607100137	9.240000e-06	62.1
41	TraesCS3A01G032500	chr5A	92.857	42	3	0	2093	2134	476653230	476653189	9.240000e-06	62.1

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS3A01G032500	chr3A	18817917	18821003	3086	False	5701	5701	100.000	1	3087	1	chr3A.!!$F1	3086
1	TraesCS3A01G032500	chr3A	19264975	19269652	4677	True	2257	3858	97.922	1	2095	2	chr3A.!!$R1	2094
2	TraesCS3A01G032500	chr3A	745905249	745905872	623	False	723	723	87.981	2479	3087	1	chr3A.!!$F3	608
3	TraesCS3A01G032500	chr3D	17698205	17699365	1160	False	1797	1797	94.588	924	2087	1	chr3D.!!$F1	1163
4	TraesCS3A01G032500	chr3D	17342023	17343131	1108	True	1120	1120	85.175	1000	2093	1	chr3D.!!$R1	1093
5	TraesCS3A01G032500	chr3D	587475261	587475888	627	False	749	749	88.784	2477	3085	1	chr3D.!!$F2	608
6	TraesCS3A01G032500	chr6D	417750977	417752071	1094	True	1064	1064	84.349	1005	2093	1	chr6D.!!$R1	1088
7	TraesCS3A01G032500	chr6D	417775857	417776938	1081	False	942	942	82.684	1003	2087	1	chr6D.!!$F1	1084
8	TraesCS3A01G032500	chr6B	626643906	626645017	1111	False	1003	1003	83.244	992	2087	1	chr6B.!!$F2	1095
9	TraesCS3A01G032500	chr6B	2806104	2806721	617	True	736	736	88.517	2476	3085	1	chr6B.!!$R1	609
10	TraesCS3A01G032500	chr6B	309686036	309686654	618	False	728	728	88.320	2478	3085	1	chr6B.!!$F1	607
11	TraesCS3A01G032500	chr6B	626488565	626489330	765	True	728	728	84.026	1334	2093	1	chr6B.!!$R2	759
12	TraesCS3A01G032500	chr6A	560191778	560192872	1094	True	998	998	83.258	1005	2093	1	chr6A.!!$R2	1088
13	TraesCS3A01G032500	chr6A	560444263	560445332	1069	False	837	837	81.125	1003	2087	1	chr6A.!!$F1	1084
14	TraesCS3A01G032500	chr6A	473571530	473572138	608	True	704	704	87.967	2490	3087	1	chr6A.!!$R1	597
15	TraesCS3A01G032500	chr1D	101104528	101105157	629	False	782	782	89.524	2476	3087	1	chr1D.!!$F1	611
16	TraesCS3A01G032500	chr1D	476402745	476403354	609	True	649	649	86.240	2478	3085	1	chr1D.!!$R2	607
17	TraesCS3A01G032500	chr2A	25096814	25097431	617	True	774	774	89.677	2483	3087	1	chr2A.!!$R1	604
18	TraesCS3A01G032500	chr1A	440147701	440148309	608	True	708	708	88.052	2493	3087	1	chr1A.!!$R1	594
19	TraesCS3A01G032500	chr1A	549124427	549125016	589	True	643	643	86.230	2476	3085	1	chr1A.!!$R2	609
20	TraesCS3A01G032500	chr1B	16777388	16778009	621	False	706	706	87.640	2476	3079	1	chr1B.!!$F1	603
21	TraesCS3A01G032500	chr3B	825636820	825637423	603	True	664	664	86.872	2485	3085	1	chr3B.!!$R1	600
22	TraesCS3A01G032500	chrUn	319123767	319124385	618	True	603	603	85.191	2494	3085	1	chrUn.!!$R1	591
23	TraesCS3A01G032500	chrUn	375367246	375367803	557	True	582	582	86.243	2494	3033	1	chrUn.!!$R2	539
24	TraesCS3A01G032500	chr4A	646515391	646516012	621	False	569	569	83.943	2476	3076	1	chr4A.!!$F1	600

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
2093	4711	0.457035	GGGGCGTTCGTGATGTACTA	59.543	55.0	0.0	0.0	0.0	1.82	F

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability	Orientation
3068	5756	1.069765	AATACCGGCAGATCAGCGG	59.93	57.895	15.68	15.68	35.37	5.52	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

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Position	MSA Position	Penalty	Sequence	TM	GC	End Stability
2093	4711	0.457035	GGGGCGTTCGTGATGTACTA	59.543	55.000	1.82
2094	4712	1.553308	GGGCGTTCGTGATGTACTAC	58.447	55.000	2.73
2095	4713	1.133790	GGGCGTTCGTGATGTACTACT	59.866	52.381	2.57
2096	4714	2.416431	GGGCGTTCGTGATGTACTACTT	60.416	50.000	2.24
2097	4715	2.850647	GGCGTTCGTGATGTACTACTTC	59.149	50.000	3.01
2098	4716	2.850647	GCGTTCGTGATGTACTACTTCC	59.149	50.000	3.46
2099	4717	3.427233	GCGTTCGTGATGTACTACTTCCT	60.427	47.826	3.36
2100	4718	4.730657	CGTTCGTGATGTACTACTTCCTT	58.269	43.478	3.36
2101	4719	5.159209	CGTTCGTGATGTACTACTTCCTTT	58.841	41.667	3.11
2102	4720	5.060569	CGTTCGTGATGTACTACTTCCTTTG	59.939	44.000	2.77
2103	4721	5.717078	TCGTGATGTACTACTTCCTTTGT	57.283	39.130	2.83
2104	4722	5.706916	TCGTGATGTACTACTTCCTTTGTC	58.293	41.667	3.18
2105	4723	4.863131	CGTGATGTACTACTTCCTTTGTCC	59.137	45.833	4.02
2106	4724	5.176592	GTGATGTACTACTTCCTTTGTCCC	58.823	45.833	4.46
2107	4725	4.841813	TGATGTACTACTTCCTTTGTCCCA	59.158	41.667	4.37
2108	4726	5.487488	TGATGTACTACTTCCTTTGTCCCAT	59.513	40.000	4.00
2109	4727	6.670464	TGATGTACTACTTCCTTTGTCCCATA	59.330	38.462	2.74
2110	4728	6.938698	TGTACTACTTCCTTTGTCCCATAA	57.061	37.500	1.90
2111	4729	7.504926	TGTACTACTTCCTTTGTCCCATAAT	57.495	36.000	1.28
2112	4730	8.612486	TGTACTACTTCCTTTGTCCCATAATA	57.388	34.615	0.98
2113	4731	9.220906	TGTACTACTTCCTTTGTCCCATAATAT	57.779	33.333	1.28
2147	4765	7.406031	TTTTACACTAGTATGAGACAGAGGG	57.594	40.000	4.30
2148	4766	4.864483	ACACTAGTATGAGACAGAGGGA	57.136	45.455	4.20
2149	4767	4.787551	ACACTAGTATGAGACAGAGGGAG	58.212	47.826	4.30
2150	4768	4.228666	ACACTAGTATGAGACAGAGGGAGT	59.771	45.833	3.85

Showing 1 to 25 of 208 entries

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Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability
2122	4740	7.672660	TCCCTCTGTCTCATACTAGTGTAAAAA	59.327	37.037	5.39	31.80	1.94
2123	4741	7.179966	TCCCTCTGTCTCATACTAGTGTAAAA	58.820	38.462	5.39	31.80	1.52
2124	4742	6.728411	TCCCTCTGTCTCATACTAGTGTAAA	58.272	40.000	5.39	31.80	2.01
2125	4743	6.069556	ACTCCCTCTGTCTCATACTAGTGTAA	60.070	42.308	5.39	31.80	2.41
2126	4744	5.429109	ACTCCCTCTGTCTCATACTAGTGTA	59.571	44.000	5.39	0.00	2.90
2127	4745	4.228666	ACTCCCTCTGTCTCATACTAGTGT	59.771	45.833	5.39	0.00	3.55
2128	4746	4.787551	ACTCCCTCTGTCTCATACTAGTG	58.212	47.826	5.39	0.00	2.74
2129	4747	5.668535	AGTACTCCCTCTGTCTCATACTAGT	59.331	44.000	0.00	0.00	2.57
2130	4748	5.995282	CAGTACTCCCTCTGTCTCATACTAG	59.005	48.000	0.00	0.00	2.57
2131	4749	5.429109	ACAGTACTCCCTCTGTCTCATACTA	59.571	44.000	0.00	40.28	1.82
2132	4750	4.228666	ACAGTACTCCCTCTGTCTCATACT	59.771	45.833	0.00	40.28	2.12
2133	4751	4.528920	ACAGTACTCCCTCTGTCTCATAC	58.471	47.826	0.00	40.28	2.39
2134	4752	4.864483	ACAGTACTCCCTCTGTCTCATA	57.136	45.455	0.00	40.28	2.15
2135	4753	3.748645	ACAGTACTCCCTCTGTCTCAT	57.251	47.619	0.00	40.28	2.90
2136	4754	4.652679	TTACAGTACTCCCTCTGTCTCA	57.347	45.455	0.00	42.77	3.27
2137	4755	5.243283	TGTTTTACAGTACTCCCTCTGTCTC	59.757	44.000	0.00	42.77	3.36
2138	4756	5.145564	TGTTTTACAGTACTCCCTCTGTCT	58.854	41.667	0.00	42.77	3.41
2139	4757	5.464030	TGTTTTACAGTACTCCCTCTGTC	57.536	43.478	0.00	42.77	3.51
2140	4758	5.881923	TTGTTTTACAGTACTCCCTCTGT	57.118	39.130	0.00	45.21	3.41
2141	4759	5.122396	GCATTGTTTTACAGTACTCCCTCTG	59.878	44.000	0.00	37.65	3.35
2142	4760	5.221843	TGCATTGTTTTACAGTACTCCCTCT	60.222	40.000	0.00	0.00	3.69
2143	4761	5.001232	TGCATTGTTTTACAGTACTCCCTC	58.999	41.667	0.00	0.00	4.30
2144	4762	4.980573	TGCATTGTTTTACAGTACTCCCT	58.019	39.130	0.00	0.00	4.20
2145	4763	5.699097	TTGCATTGTTTTACAGTACTCCC	57.301	39.130	0.00	0.00	4.30
2146	4764	7.145932	AGATTGCATTGTTTTACAGTACTCC	57.854	36.000	0.00	0.00	3.85

Showing 1 to 25 of 234 entries

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Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.